The probes used in fluorescence-based assays/imaging have the distinct advantage of reducing non-specific signals and bypassing scattering, giving them an edge over other imaging techniques. At the core of this lies, the fluorophores (proteins and dyes) with unique chemistry and unique mechanisms. This is specifically true with fluorophores that are photoactivable/photoconvertible/photoswitchable. Molecular cloning and conjugation methods allow the tethering of these probes with biomolecules and proteins of interest and their targeted delivery to the organelle of activity. The conversion of one to another form occurs through a photochemical process whereby small chemical groups is removed or modified. For example, Cy5 converts to Cy3 via novel excision of \(C_2 H_2\) from the polymethine chain. Another mechanism for photoconversion involves the conformation of arginine at residue 66 by threonine at residue 69 of fluorescent proteins from Anthozoan families (Dendra2, maple, Eos, mKikGR, pcDronpa protein families). Some fluorescent proteins like wt-GFP exist in two forms: neutral and anionic, of which one form (mostly anionic) is fluorescent. These fluorescent proteins often link through hydrogen bonds to other proteins of interest/biological macromolecules, making it the most desired probe for live cell/organism imaging. In some photoswitchable proteins (IrisFP and Dronpa), a unique mechanism takes place where Cis-Trans isomerization of the chromophore results in photoconversion. In this chapter, we will focus on the photochemistry of these unique fluorescent probes and discuss their mechanism of action, which gives them central stage in super-resolution imaging.